Analysis and Workflow Tools

The All of Us Researcher Workbench supports a variety of cloud-based applications to analyze All of Us participant data (Jupyter Notebook, RStudio, and SAS Studio) and to manage workflows (Cromwell and Nextflow)

These applications incur costs as they utilize cloud environments, which are virtual spaces that allow users to access and manage computing resources over the internet. Read what to know about costs and how to pay for research analysis.

Jupyter Notebook

Jupyter Notebook is a popular tool used by data scientists, researchers, and developers for interactive computing and data analysis. Jupyter Notebook provides an environment where you can write and execute code, visualize data, and document your work in a single document. Programming languages R or Python are available for Jupyter Notebook in the Researcher Workbench.

RStudio

RStudio is an integrated development environment (IDE) for researchers using programming language R for statistical computing and graphics. RStudio provides a user-friendly interface that makes it easier for users to write, debug, and execute R code. Programming language R is available for RStudio in the Researcher Workbench.

SAS Studio

SAS Studio is a statistical software tool used by researchers for data analysis and statistical modeling. SAS Studio has the ability to handle large datasets efficiently with an extensive set of statistical techniques and a user-friendly interface. Programming language SAS is available for SAS Studio in the Researcher Workbench.

Cromwell and Nextflow

The Researcher Workbench supports two workflow engines: Cromwell and Nextflow.

• Cromwell is a workflow management system that is designed to help scientists and researchers organize and execute complex computational workflows. Cromwell provides a platform for defining, running, and monitoring workflows, making it easier to manage and automate scientific analyses. Cromwell application can be readily found in the workspace analysis panel.
• Nextflow is a workflow engine that uses a DSL (Groovy with workflow-specific extensions).

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